Two cell lines (CT26 colon carcinoma and 4T1 breast cancer) Two organs (spleen and tumors) With and without checkpoint inhibitor treatment
Now selection criteria is rank < 2% and expression > 0.1 TPM - top 500 neoepitopes Can these selection critereia be optimized
Data set is to small to see a clear pattern in immnunugenic and non-immunugenic neoepitopes Also shown by a poor performance of the model But! With a trend that if we take into account multiple neoepitope characteristics, we can improve immunogenic selection Further work: Try out with more data, when more peptides are screened Is the results the same for human data Make packages for human data